[BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?

[Moshe Olshansky]

Hi Rich,

Whether to use the moderated t-statistic or not does not depend on whether
you are interested in the 10 particular genes or in all differentially
expressed ones. This will affect your multiple testing adjustment.
The simplest way for you to proceed is to use limma as usual, get the
topTable but then take the UNADJUSTED p-values for your 10 genes of
interest and use the p.adjust function to adjust for multiple testing if
you wish. In any case you should also look at (log)Fold Changes.

Best regards,
Moshe.


> Dear Bioconductor  List.
>
> 	I am using Limma to analyze differential expression between 2
> conditions on an Affy chip.
> My experimental collaborator asks for the differential  expression of
> 10 predefined genes.
>
> A, Should I correct for false discoveries based upon all of the genes
> on the chip?
> B. If not, should I correct for false discoveries just for the
> probeids for the 10 predefined
> genes?
> C. Should I use the moderated t-statistic or just use an unmoderated t-
> test for those 10
> genes.
>
> Thanks and best wishes,
> Rich
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
>
> "School is an evil plot to suppress my individuality"
>
> Rose Friedman, age15
>
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-- 
Moshe Olshansky
Division of Bioinformatics
The Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052
e-mail: olshansky at wehi.edu.au
tel: (03) 9345 2849


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